rdkit - Analyze and manipulate molecules with RDKit
Provides Python APIs for parsing, analyzing, searching, comparing, visualizing, and transforming molecular structures and reactions.
Tags
Updated: 2026-10-07Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Parse molecular structures
- Write molecular representations
- Sanitize and validate molecules
- Calculate molecular descriptors
- Generate molecular fingerprints
- Compute molecular similarity
- Search molecular substructures
- Generate chemical reactions
- Generate 2D and 3D coordinates
- Analyze stereochemistry and fragments
- Visualize molecules
Inputs
- Molecular structures
- SMILES, SDF, MOL, and InChI data
- SMARTS queries
- Reaction SMARTS
- Molecular datasets
Outputs
- Parsed molecule objects
- Molecular representations
- Calculated descriptors
- Molecular fingerprints
- Similarity scores
- Substructure matches
- Reaction products
- 2D and 3D coordinates
- Molecular visualizations
- Validation messages
Requirements
- Python runtime
- RDKit library